Crystal Packing Interactions Research Articles

2-(3-Cyano-4-methyl-5,5-diphenyl-5H-furan-2-ylidene)malononitrile

The title compound, C21H13N3O, crystallizes with two independent molecules with similar conformations per asymmetric unit. The dihydrofuran rings are essentially planar with maximum deviations of 0.017 (1) and 0.006 (1) Å for the O atoms. The dihedral angles between the di­hydro­furan ring and the attached phenyl rings are 79.90 (6) and 82.07 (6)° in one mol­ecule and 79.36 (6) and 72.26 (6)° in the other. In the crystal, the molecules are linked by weak C—H⋯π and C—H⋯N inter­actions similar to those in other closely related crystals. The replacement of appended methyl by phenyl groups has not significantly affected the dihydrofuran ring structure or the crystal packing interactions.

Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase

Homogentisate 1,2-dioxygenase (HGDO) uses a mononuclear nonheme Fe(2+) to catalyze the oxidative ring cleavage in the degradation of Tyr and Phe by producing maleylacetoacetate from homogentisate (2,5-dihydroxyphenylacetate). Here, we report three crystal structures of HGDO, revealing five different steps in its reaction cycle at 1.7-1.98 Å resolution. The resting state structure displays an octahedral coordination for Fe(2+) with two histidine residues (His331 and His367), a bidentate carboxylate ligand (Glu337), and two water molecules. Homogentisate binds as a monodentate ligand to Fe(2+), and its interaction with Tyr346 invokes the folding of a loop over the active site, effectively shielding it from solvent. Binding of homogentisate is driven by enthalpy and is entropically disfavored as shown by anoxic isothermal titration calorimetry. Three different reaction cycle intermediates have been trapped in different HGDO subunits of a single crystal showing the influence of crystal packing interactions on the course of enzymatic reactions. The observed superoxo:semiquinone-, alkylperoxo-, and product-bound intermediates have been resolved in a crystal grown anoxically with homogentisate, which was subsequently incubated with dioxygen. We demonstrate that, despite different folds, active site architectures, and Fe(2+) coordination, extradiol dioxygenases can proceed through the same principal reaction intermediates to catalyze the O2-dependent cleavage of aromatic rings. Thus, convergent evolution of nonhomologous enzymes using the 2-His-1-carboxylate facial triad motif developed different solutions to stabilize closely related intermediates in unlike environments.

Elastic and inelastic diffraction changes upon variation of the relative humidity environment of PurE crystals

The different changes observed in the diffraction patterns of three different crystal forms (hexagonal, trigonal and monoclinic) of PurE (EC 4.1.1.21), an enzyme from the purine-biosynthesis pathway of Bacillus anthracis, upon a wide range of changes in the relative humidity environment of the crystals are documented. In addition, the changes in the unit-cell parameters, volume and bulk solvent in the three different crystal forms were systematically followed. In an attempt to explain the elastic (P6(5)22) and inelastic (P3(1)21) changes in the diffraction pattern, refined structures of the three different crystal forms determined at 100 K are presented, with particular emphasis on the tertiary and quaternary structural differences, crystal packing, intermolecular and intramolecular interactions and solvent structure. The refined structures show that the precipitant salts, solvent structure (both ordered and bulk) and conformation of the C-termini all play a role in creating a unique cement at both the intramolecular and intermolecular contacts of the different crystal forms. It is suggested that it is the combination of polyethylene glycol and the structure of the ordered water molecules (first and second layers) as well as the structure of the bulk solvent that are the critical factors in the plasticity of the hexagonal crystal packing as opposed to the inelastic responses of the lower symmetry forms.

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 μs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.

Crystal Structure Optimization and Semi-Empirical Quantum Chemical Calculations of N-(3,4-Dichlorophenyl)-3-Oxo-Butanamide

The crystal structure of N-(3,4-Dichlorophenyl)-3-oxobutanamide (I) is optimized by semi-empirical methods using MOPAC2009 program. The optimized geometries from both Austin Model 1 (AM1) and Parametrization Model 6 (PM6) describe the conformational discrepancy and crystal packing. The energy minimized structures from both the models are in good agreement with X-ray crystal data. The intramolecular charge transfer interactions are studied from the molecular orbital calculations. The parametric molecular electrostatic potential (PMEP) calculated by AM1 semi-empirical method shows the involvement of oxygen and chlorine atoms in the crystal packing interactions. The aromaticity of phenyl ring in the structure is determined using HOMED calculations.

The Crystal Structure of the Catalytic Domain of the NF-κB Inducing Kinase Reveals a Narrow but Flexible Active Site

The NF-κB inducing kinase (NIK) regulates the non-canonical NF-κB pathway downstream of important clinical targets including BAFF, RANKL, and LTβ. Despite numerous genetic studies associating dysregulation of this pathway with autoimmune diseases and hematological cancers, detailed molecular characterization of this central signaling node has been lacking. We undertook a systematic cloning and expression effort to generate soluble, well-behaved proteins encompassing the kinase domains of human and murine NIK. Structures of the apo NIK kinase domain from both species reveal an active-like conformation in the absence of phosphorylation. ATP consumption and peptide phosphorylation assays confirm that phosphorylation of NIK does not increase enzymatic activity. Structures of murine NIK bound to inhibitors possessing two different chemotypes reveal conformational flexibility in the gatekeeper residue controlling access to a hydrophobic pocket. Finally, a single amino acid difference affects the ability of some inhibitors to bind murine and human NIK with the same affinity.

Synthesis, structural and biological characterization of 5-phenylhydantoin derivatives as potential anticonvulsant agents

Considering the importance of hydantoin derivatives in treatment of status epilepticus, four 5-phen- ylhydantoins, whose lipophilicities were estimated to be similar to that of phenytoin, were synthesized. Evaluation of their anticonvulsant activities was performed on rats by subcutaneous pentylenetetrazol seizure test and intravenous pentylenetetrazol threshold test, and spontaneous locomo- tor activity test was used to assess possible sedative effects. X-ray analysis of three compounds suggested that certain analogies might be drawn between interactions in crystal packing and biological interactions responsible for their anticonvulsant activity. It was found that 5-ethyl-5-phenyl- 3-propylhydantoin exhibits the most favorable pharmaco- logical properties among the synthesized compounds, i.e., anticonvulsant activity comparable to phenytoin with lower liability for induction of sedation in rats.

Synthesis, Crystal Structure and Hirshfeld Surface Analysis of [Cu(EDTB)][CdBr4]·H2O (EDTB = N,N,N′,N′-tetrakis-[(2-benzimidazolyl)methyl]-1,2-ethanediamine)

N,N,N′,N′-tetrakis-[(2-benzimidazolyl)methyl]-1,2-ethanediamine (EDTB), a multidentate ligand, was synthesized by refluxing of EDTA and o-phenylenediamine in glycol with a molar ratio of 1:4. Reaction of the 2:1:1 stoichiometric proportion of EDTB with cadmium(II) bromide and copper(II) bromide in methanol and distilled water affords a mononuclear copper(II) complex, [Cu(EDTB)][CdBr4]·H2O (1), which crystallizes in the monoclinic space group P21/c with a = 12.226(3), b = 20.948(5), c = 19.330(3) A, β = 116.597(11)°, V = 4426.7(17) A3 and Z = 4. [Cu(EDTB)]2+ cations are linked to the [CdBr4]2− anions and water molecules by N–H···Br and N–H···O hydrogen bonds. Furthermore, C–H···Br, C–H···π and π···π weak interactions also connect these units into a 2D structure. A detailed investigation of the crystal packing and intermolecular interactions has been examined using the Hirshfeld surface analysis. Hirshfeld surfaces and fingerprint plots showed the presence of intermolecular interactions. Various weak interactions in a Cu–EDTB complex [Cu(EDTB)][CdBr4]·H2O connect each unit into an attractive 2D structure.

First principles investigation of L-alanine in terahertz region

Terahertz absorption spectrum (0.5-4.0THz) of L-alanine in the solid phase was measured by terahertz time-domain spectroscopy at room temperature. Simulations utilizing gaseous-state and solid-state theory were performed to determine the origins of the observed vibrational features. Our calculations showed that the measured features in solid-state materials could be well understood by considering the crystal packing interactions in a solid-state density functional theory calculation. Furthermore, intermolecular vibrations of L-alanine are found to be the dominating contributions to these measured spectral features in the range of 0.5-4.0THz, except that located at 3.11THz.

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites

The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists, how interactions can be verified and predicted by computational approaches using available data on protein structural complexes. Recently we developed an approach called IBIS (Inferred Biomolecular Interaction Server) to predict and annotate protein-protein binding sites and interaction partners, which is based on the assumption that the structural location and sequence patterns of protein-protein binding sites are conserved between close homologs. In this study first we confirmed high accuracy of our method and found that its accuracy depends critically on the usage of all available data on structures of homologous complexes, compared to the approaches where only a non-redundant set of complexes is employed. Second we showed that there exists a trade-off between specificity and sensitivity if we employ in the prediction only evolutionarily conserved binding site clusters or clusters supported by only one observation (singletons). Finally we addressed the question of identifying the biologically relevant interactions using the homology inference approach and demonstrated that a large majority of crystal packing interactions can be correctly identified and filtered by our algorithm. At the same time, about half of biological interfaces that are not present in the protein crystallographic asymmetric unit can be reconstructed by IBIS from homologous complexes without the prior knowledge of crystal parameters of the query protein.

An unprecedented “linear-bent” isomerism in tri-nuclear Cu2IIZnII complexes with a salen type di-Schiff base ligand

Two new trinuclear hetero-metallic copper(II)-zinc(II) complexes [(CuL)(2)Zn(N(3))(2)] (1A and 1B) have been synthesized using [CuL] as a so-called "metalloligand" (where H(2)L = N,N'-bis(salicylidene)-1,3-propanediamine) and structurally characterized. Complexes 1A and 1B have the same molecular formula but crystallize in different crystal systems (triclinic for 1A and monoclinic for 1B) with space group P1 for 1A and P2(1)/c for 1B. 1A is an angular trinuclear species, in which two terminal four-coordinate square planar "metalloligand" [CuL] are coordinated to a central Zn(II) through double phenoxido bridges. The Zn(II) is in a six-coordinate distorted octahedral environment being bonded additionally to two mutually cis nitrogen atoms of terminal azide ions. In complex 1B, in addition to the double phenoxido bridge, the two terminal Cu(II) ions are linked to the central Zn(II) via a μ(-l,l) azido bridge giving rise to a square pyramidal environment around the Cu(II) ions and consequently the structure becomes linear. These two species can be considered as "linear-bent" isomers. EPR spectra and ESI mass spectra show that the two isomers are identical in solution. The DFT calculation reveals that the energy of 1A is 7.06 kcal mol(-1) higher than that of 1B. The existence of both isomers in the solid state suggests that crystal packing interactions in are more efficient and probably compensate for the difference in energy.

Participation of protein sequence termini in crystal contacts

The analysis of the crystal packing interactions, in a nonredundant set of high resolution and monomeric globular protein crystal structures, shows that the residues located at the N- and C-termini of the sequence tend to participate in packing interaction more often than expected and that often they interact with each other. Since the sequence termini are, in general, conformationally very flexible and since they host electrical charges of opposite sign, it can be hypothesized that they play a crucial role in the early formation of the nonphysiological contacts that bring to protein crystallization. It is thus not surprising that modest lengthening/shortening of the sequence termini have often a dramatic effect on protein crystallogenesis.

The Role of MukE in Assembling a Functional MukBEF Complex

The MukB–MukE–MukF protein complex is essential for chromosome condensation and segregation in Escherichia coli. The central component of this complex, the MukB protein, is related functionally and structurally to the ubiquitous SMC ( structural maintenance of chromosomes) proteins. In a manner similar to SMC, MukB requires the association of two accessory proteins (MukE and MukF) for its function. MukF is a constitutive dimer that bridges the interaction between MukB and MukE. While MukB can condense DNA on its own, it requires MukF and MukE to ensure proper chromosome segregation. Here, we present a novel structure of the E. coli MukE–MukF complex, in which the intricate crystal packing interactions reveal an alternative MukE dimerization interface spanning both N- and C-terminal winged-helix domains of the protein. The structure also unveils additional cross-linking interactions between adjacent MukE–MukF complexes mediated by MukE. A variant of MukE encompassing point mutations on one of these surfaces does not affect assembly of the MukB–MukE–MukF complex and yet cannot restore the temperature sensitivity of the mukE∷ kan strain, suggesting that this surface may mediate critical protein–protein interactions between MukB–MukE–MukF complexes. Since the dimerization interface of MukE overlaps with the region of the protein that interacts with MukB in the MukB–MukE–MukF complex, we suggest that competing MukB–MukE and MukE–MukE interactions may regulate the formation of higher-order structures of bacterial condensin.

Dispersed disease-causing neomorphic mutations on a single protein promote the same localized conformational opening

The question of how dispersed mutations in one protein engender the same gain-of-function phenotype is of great interest. Here we focus on mutations in glycyl-tRNA synthetase (GlyRS) that cause an axonal form of Charcot-Marie-Tooth (CMT) diseases, the most common hereditary peripheral neuropathies. Because the disease phenotype is dominant, and not correlated with defects in the role of GlyRS in protein synthesis, the mutant proteins are considered to be neomorphs that gain new functions from altered protein structure. Given that previous crystal structures showed little conformational difference between dimeric wild-type and CMT-causing mutant GlyRSs, the mutant proteins were investigated in solution by hydrogen-deuterium exchange (monitored by mass spectrometry) and small-angle X-ray scattering to uncover structural changes that could be suppressed by crystal packing interactions. Significantly, each of five spatially dispersed mutations induced the same conformational opening of a consensus area that is mostly buried in the wild-type protein. The identified neomorphic surface is thus a candidate for making CMT-associated pathological interactions, and a target for disease correction. Additional result showed that a helix-turn-helix WHEP domain that was appended to GlyRS in metazoans can regulate the neomorphic structural change, and that the gain of function of the CMT mutants might be due to the loss of function of the WHEP domain as a regulator. Overall, the results demonstrate how spatially dispersed and seemingly unrelated mutations can perpetrate the same localized effect on a protein.

Two distinct conformations of helix 6 observed in antagonist-bound structures of a β 1 -adrenergic receptor

The β(1)-adrenergic receptor (β(1)AR) is a G-protein-coupled receptor whose inactive state structure was determined using a thermostabilized mutant (β(1)AR-M23). However, it was not thought to be in a fully inactivated state because there was no salt bridge between Arg139 and Glu285 linking the cytoplasmic ends of transmembrane helices 3 and 6 (the R(3.50) - D/E(6.30) "ionic lock"). Here we compare eight new structures of β(1)AR-M23, determined from crystallographically independent molecules in four different crystals with three different antagonists bound. These structures are all in the inactive R state and show clear electron density for cytoplasmic loop 3 linking transmembrane helices 5 and 6 that had not been seen previously. Despite significantly different crystal packing interactions, there are only two distinct conformations of the cytoplasmic end of helix 6, bent and straight. In the bent conformation, the Arg139-Glu285 salt bridge is present, as in the crystal structure of dark-state rhodopsin. The straight conformation, observed in previously solved structures of β-receptors, results in the ends of helices 3 and 6 being too far apart for the ionic lock to form. In the bent conformation, the R(3.50)-E(6.30) distance is significantly longer than in rhodopsin, suggesting that the interaction is also weaker, which could explain the high basal activity in β(1)AR compared to rhodopsin. Many mutations that increase the constitutive activity of G-protein-coupled receptors are found in the bent region at the cytoplasmic end of helix 6, supporting the idea that this region plays an important role in receptor activation.

From Crystal Packing to Molecular Recognition: Prediction and Discovery of a Binding Site on the Surface of Polo‐Like Kinase 1

Picking the pocket: Crystal-packing interactions are present in every macromolecular structure solved with X-ray methods; however, they have not been extensively used to gain insight into molecular recognition. A novel approach is described to utilize these packing interactions for the discovery of a flexible binding site and ligands recognized by it (see picture).

Role of Hetero-Halogen (F···X, X = Cl, Br, and I) or Homo-Halogen (X···X, X = F, Cl, Br, and I) Interactions in Substituted Benzanilides

A series of halogen-substituted benzanilides have been synthesized and characterized, and crystallization studies directed toward generation of polymorphs have been performed to delineate the importance of interactions involving halogens. The effect of halogen substitution on the molecular conformation and supramolecular packing has been investigated. The N−H···O H-bond is a key structure-directing element acting in conjunction with C−H···O and C−H···π interactions. In addition, it is of importance to note that organic fluorine prefers Type I F···F contacts, whereas Cl, Br, and I prefer Type II contacts. Hetero-halogen···halogen interactions on the other hand are predominately of Type II geometry, and this is due to the greater polarizability of the electron density associated with the heavier halogens. It is of importance to evaluate the contributing role of these interactions in crystal structure packing and the co-operativity associated with such interactions in the solid state.

X-Ray diffraction and vibrational spectroscopic study of 2-chloro-N-{4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]-thiazol-2-yl}-acetamide

The title compound C18H21ClN2SO crystallizes with Z = 4 in space group P21/c. The structure of the title compound was characterized by 1H-NMR, 13C-NMR, IR and single crystal diffraction. There are an intermolecular N-H…O hydrogen bond and a C-H…π interactions in crystal packing. In addition to the molecular geometry and packing obtained from X-ray experiment, the molecular geometry and vibrational frequencies of the title compound in ground state have been calculated using density functional theory method DFT (B3LYP) with 6-31G (d, p) basis set. Calculated frequencies, bond lengths, angles and dihedral angles are in good agreement with the corresponding experimental data.

Multiple C-terminal tail Ca2+/CaMs regulate CaV1.2 function but do not mediate channel dimerization

Interactions between voltage-gated calcium channels (Ca(V)s) and calmodulin (CaM) modulate Ca(V) function. In this study, we report the structure of a Ca(2+)/CaM Ca(V)1.2 C-terminal tail complex that contains two PreIQ helices bridged by two Ca(2+)/CaMs and two Ca(2+)/CaM-IQ domain complexes. Sedimentation equilibrium experiments establish that the complex has a 2:1 Ca(2+)/CaM:C-terminal tail stoichiometry and does not form higher order assemblies. Moreover, subunit-counting experiments demonstrate that in live cell membranes Ca(V)1.2s are monomers. Thus, contrary to previous proposals, the crystallographic dimer lacks physiological relevance. Isothermal titration calorimetry and biochemical experiments show that the two Ca(2+)/CaMs in the complex have different properties. Ca(2+)/CaM bound to the PreIQ C-region is labile, whereas Ca(2+)/CaM bound to the IQ domain is not. Furthermore, neither of lobes of apo-CaM interacts strongly with the PreIQ domain. Electrophysiological studies indicate that the PreIQ C-region has a role in calcium-dependent facilitation. Together, the data show that two Ca(2+)/CaMs can bind the Ca(V)1.2 tail simultaneously and indicate a functional role for Ca(2+)/CaM at the C-region site.

The 19-Amino Acid Insertion in the Tumor-associated Splice Isoform Rac1b Confers Specific Binding to p120 Catenin

The Rac1b splice isoform contains a 19-amino acid insertion not found in Rac1; this insertion leads to decreased GTPase activity and reduced affinity for GDP, resulting in the intracellular predominance of GTP-bound Rac1b. Here, using co-precipitation and proteomic methods, we find that Rac1b does not bind to many common regulators of Rho family GTPases but that it does display enhanced binding to SmgGDS, RACK1, and p120 catenin (p120(ctn)), proteins involved in cell-cell adhesion, motility, and transcriptional regulation. We use molecular modeling and structure analysis approaches to determine that the interaction between Rac1b and p120(ctn) is dependent upon protein regions that are predicted to be unstructured in the absence of molecular complex formation, suggesting that the interaction between these two proteins involves coupled folding and binding. We also find that directed cell movement initiated by Rac1b is dependent upon p120. These results define a distinct binding functionality of Rac1b and provide insight into how the distinct phenotypic program activated by this protein may be implemented through molecular recognition of effectors distinct from those of Rac1.